When I was using an MBP and a Windows desktop, I got a gaming keyboard that let you remap the keys. I swapped the keycaps on the keyboard so that the Control key was where the Command key would be. Of course, this doesn't help if you're using a laptop, but my desktop keyboard remained that way for a while, even after I left OSX on the laptop side.

With respect to Windows on the Macbook Pro, when I used Windows VMs, I would go to the VM preferences and swap the command key mappings so that I could continue using my muscle memory.